Diacylglycerol acyltransferase (DGAT) and acyl-CoA: cholesterol acyltransferase (ACAT) are the enzymes that catalyze the final reactions of triacylgycerol (TG) and cholesteryl ester (CE) synthesis, and accumulation of TG and CE in adipocytes and arteries causes obesity and atherosclerosis, respectively. Therefore, DGAT and ACAT have been viewed as potential therapeutic targets for these diseases. From the screening program for DGAT inhibitors, new compounds were discovered from fungal and plant extracts, and are expected to provide leads for drug development. From the screening programs for ACAT inhibitors and lipid droplet synthesis inhibitors, new compounds with chemical structures different from those of known synthetic inhibitors were discovered from the cultures of fungal and actinomycete strains. Among them, fungal beauveriolide III rather selectively inhibited ACAT1 isozyme, while fungal pyripyropene A was found to be a highly selective inhibitor of ACAT2 isozyme. Both inhibitors proved orally active in in vivo models. Furthermore, a library of beauveriolide and pyripyropene analogs was prepared by combinatorial and semisynthetic methods, respectively. The future prospects of these inhibitors are discussed.